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Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V9D PDB ENTRY 2V9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 100 MM HEPES PH 6.5, 200 MM MGCL2, 25% PEG 3350, RT
Crystal Properties Matthews coefficient Solvent content 2.09 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.689 α = 90 b = 156.494 β = 90 c = 55.884 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS-IV MIRRORS 2006-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.09 50 99.4 0.14 6.1 6.7 73987 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.16 96.3 0.59 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V9D 2.2 19.92 60553 3252 99.8 0.192 0.19 0.1896 0.232 0.2313 RANDOM 5.45
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.08 -0.07 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.857 r_dihedral_angle_4_deg 19.034 r_dihedral_angle_3_deg 17.3 r_dihedral_angle_1_deg 12.53 r_scangle_it 3.03 r_scbond_it 2.017 r_angle_refined_deg 1.788 r_mcangle_it 0.969 r_mcbond_it 0.702 r_symmetry_vdw_refined 0.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.857 r_dihedral_angle_4_deg 19.034 r_dihedral_angle_3_deg 17.3 r_dihedral_angle_1_deg 12.53 r_scangle_it 3.03 r_scbond_it 2.017 r_angle_refined_deg 1.788 r_mcangle_it 0.969 r_mcbond_it 0.702 r_symmetry_vdw_refined 0.363 r_nbtor_refined 0.305 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.155 r_symmetry_hbond_refined 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9014 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing